I thought the series jumped the shark after the completion of Tudi Wiggins' second story arc.
Very interesting - I have to say that, in my opinion, the second 13 weeks of the show kind of ran out of steam about 2/3 of the way through. I was very interested in the first part of the 2nd storyline, but then there seemed to be a lot of "What do we do next?" type of plot decisions (I don't want to get specific and spoil anything for anyone). Ironically, I find the last 13 weeks to be some of the most interesting, and I actually tend to disagree somewhat with the notion of the radical change in continuity. There was a shift, to be sure, but to me there are at least somewhat valid reasons for it.
On an interesting note, I actually asked Harding Lemay (the writer for the final 13 weeks) why he did what he did plotwise, and he did say it was very deliberate, as opposed to being a case of a writer unfamiliar with the previous episodes simply writing based on lack of previous continuity. Again, I don't want to spoil anything by revealing the plot twists. Sorry to be so vague, but I wouldn't want to ruin anyone's potential viewing!
One tidbit of information about the second 65 episodes - one big plotline that was dropped was the character of Cort as an evil warlock type who dabbled in necromancy in order to manipulate events to his liking. Although this is vaguely hinted at on screen, originally it formed the basis for a lot of the plotting of episodes 66-130.